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- PDB-2k5z: Solution structure and dynamics of the apical stem-loop of Duck h... -

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Basic information

Entry
Database: PDB / ID: 2k5z
TitleSolution structure and dynamics of the apical stem-loop of Duck hepatitis B virus
ComponentsDuck HBV apical loop
KeywordsRNA / HBV / Duck / apical loop / epsilon
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAmpt, K.A.M. / Tessari, M. / Wijmenga, S.S.
Citation
Journal: Biochemistry / Year: 2009
Title: The unstable part of the apical stem of duck hepatitis B virus epsilon shows enhanced base pair opening but not pico- to nanosecond dynamics and is essential for reverse transcriptase binding.
Authors: Ampt, K.A. / van der Werf, R.M. / Nelissen, F.H. / Tessari, M. / Wijmenga, S.S.
#1: Journal: To be Published
Title: 1H, 13C and 15N NMR assignments of Duck HBV apical stem loop of the epsilon encapsidation signal
Authors: Ampt, K.A.M. / Ottink, O.M. / Girard, F.C. / Nelissen, F.H.T. / Tessari, M. / Wijmenga, S.S.
History
DepositionJul 1, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Duck HBV apical loop


Theoretical massNumber of molelcules
Total (without water)9,2481
Polymers9,2481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain Duck HBV apical loop


Mass: 9248.428 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The Sequence of this RNA can be found in Duck Hepatitis B virus

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
3222D 1H-1H NOESY
2353D 1H-13C NOESY
1432D 1H-15N HSQC
2552D 1H-15N HSQC
3622D 1H-13C HSQC
3742D 1H-13C HSQC
2852D 1H-13C HSQC
3922D DQF-COSY
21052D 1H-1H COSY
21153D (H)CCH-TOCSY
21253D HCN

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 95% H2O, 5% D2O, 95% H2O/5% D2O95% H2O/5% D2O
21.2 mM Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 100% D2O, 100% D2O100% D2O
31 mM [U-13C; U-15N]-Ura Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 5% D2O, 95% H2O, 95% H2O/5% D2O95% H2O/5% D2O
41 mM [U-13C; U-15N]-Ura Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 100% D2O, 100% D2O100% D2O
50.7 mM [U-13C; U-15N] Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 5% D2O, 95% H2O, 1 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
60.7 mM [U-13C; U-15N] Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 5% D2O, 95% H2O, 15 mg/mL Pf1 phage, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMDuck HBV apical loop1
10 mMsodium phosphate buffer1
0.1 mMEDTA1
95 %H2O1
5 %D2O1
1.2 mMDuck HBV apical loop2
10 mMsodium phosphate buffer2
0.1 mMEDTA2
100 %D2O2
1 mMDuck HBV apical loop[U-13C; U-15N]-Ura3
10 mMsodium phosphate buffer3
0.1 mMEDTA3
5 %D2O3
95 %H2O3
1 mMDuck HBV apical loop[U-13C; U-15N]-Ura4
10 mMsodium phosphate buffer4
0.1 mMEDTA4
100 %D2O4
0.7 mMDuck HBV apical loop[U-13C; U-15N]5
10 mMsodium phosphate buffer5
0.1 mMEDTA5
5 %D2O5
95 %H2O5
1 mMDSS5
0.7 mMDuck HBV apical loop[U-13C; U-15N]6
10 mMsodium phosphate buffer6
0.1 mMEDTA6
5 %D2O6
95 %H2O6
15 mg/mLPf1 phage6
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1106.7ambient 278 K
2106.7ambient 288 K
3106.7ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: RDC refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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